3MSJ

Structure of bace (beta secretase) in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B8L	PDB ENTRY 2B8L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	273	10% PEG 4000, 100MM MES PH 6.0, VAPOR DIFFUSION, TEMPERATURE 273K, temperature 273 KK

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 229.196	α = 90
b = 98.829	β = 103.36
c = 63.132	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2008-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA		SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	111.8	94.7	0.053	7.2	2.2		126584

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	94.2		0.678	1	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2B8L	1.8	111.8	118247	1212	94.37	0.1775	0.17718	0.20846	RANDOM	16.593

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.96		-0.86	-1.33		2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.8
r_dihedral_angle_4_deg	21.997
r_dihedral_angle_3_deg	13.639
r_dihedral_angle_1_deg	6.833
r_scangle_it	5.177
r_scbond_it	3.94
r_mcangle_it	2.589
r_mcbond_it	2.134
r_angle_refined_deg	1.353
r_angle_other_deg	0.743
r_mcbond_other	0.554
r_symmetry_vdw_refined	0.318
r_symmetry_vdw_other	0.26
r_nbd_other	0.193
r_nbd_refined	0.19
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.131
r_nbtor_other	0.088
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8824
Nucleic Acid Atoms
Solvent Atoms	646
Heterogen Atoms	147

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling